Thanks Robbie I found what I was looking for in PDB_REDO. Thanks
Mahesh On Fri, Oct 11, 2013 at 4:49 PM, Robbie Joosten <[email protected]>wrote: > Hi Mahesh, > > They will be close but not the same. RMSDs should be very close normally, > but different treatment of hetero compounds (ligands and such), outliers > and > LINKs added during annotation may cause small deviations. The deviations in > R-factors can be much larger for all sorts of reasons. The data that is > used > now can be (slightly) different from what was used before due to different > scaling, merging of I+ and I-, conversion from F to I, outlier rejection, > R-free set annotation, deposition errors (i.e. missing data), or deposition > of all measured data, not just the data used in the final refinement (this > is actually a good thing). Different programs have different treatment of > bulk solvent. There can be rounding errors is the conversion from TLS to > anisotropic B-factors. The use of riding hydrogens can also make a big > difference. > There are several papers that discuss the sources of these R-factor > deviations, e.g. papers about EDS, PDB_REDO and phenix.model_vs_data. > > Cheers, > Robbie > > > -----Original Message----- > > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > > Mahesh Lingaraju > > Sent: Friday, October 11, 2013 21:59 > > To: [email protected] > > Subject: [ccp4bb] R and R free from CIF file deposited in PDB > > > > Hello Experts, > > > > I was wondering if the R, Rfree, RMSD for bonds and angles calculated by > > polygon plug in in PHENIX GUI using the cif file & pdb file deposited in > protein > > structure database would be the same as reported in database/publication > ? > > > > I apologize in advance if this is a PHENIX specific question. > > > > Many thanks > > > > Mahesh >
